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Nucleic Acids Res. 1998 Aug 15;26(16):3825-36.

Automatic detection of conserved RNA structure elements in complete RNA virus genomes.

Author information

  • 1Institut für Theoretische Chemie, Universität Wien, Wien, Austria, EMBL, Heidelberg, Germany, Max Delbrück Center, Berlin, Germany.

Abstract

We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and phylogenetic comparison. In contrast to purely phylogenetic methods, our algorithm can be used for small data sets of approximately 10 sequences, efficiently exploiting the information contained in the sequence variability. The procedure constructs a prediction only for those parts of sequences that are consistent with a single conserved structure. Our implementation produces reasonable consensus structures without user interference. As an example we have analysed the complete HIV-1 and hepatitis C virus (HCV) genomes as well as the small segment of hantavirus. Our method confirms the known structures in HIV-1 and predicts previously unknown conserved RNA secondary structures in HCV.

PMID:
9685502
[PubMed - indexed for MEDLINE]
PMCID:
PMC147758
Free PMC Article
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